file_tag = sprintf("%s_BL_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, USE.NAMES=FALSE, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 2.00 21.00 22.00 20.98 22.00 23.00
## [1] 40
## [1] 2 18 19 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 22 22 22 22 22 22 22
## [26] 22 22 22 22 22 22 22 22 22 23 23 23 23 23 23
bioMart.All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]alias2Symbol function from
limma.a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "SEPT2"
## [1] "SEPTIN6" "SEPTIN2"
##
## FALSE TRUE
## 1607 42
##
## FALSE TRUE <NA>
## 42 1565 42
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: C10orf91 LINC02870
## 2: C12orf10 MYG1
## 3: C12orf45 NOPCHAP1
## 4: C6orf48 SNHG32
## 5: C6orf99 LINC02901
## 6: CXorf40A EOLA1
## 7: CXorf57 RADX
## 8: FAM102A EEIG1
## 9: FAM173A ANTKMT
## 10: FAM213B PRXL2B
## 11: H2AFX H2AX
## 12: HIST1H2AG H2AC11
## 13: HIST1H2BK H2BC12
## 14: HIST1H2BN H2BC15
## 15: HIST1H3A H3C1
## 16: HIST1H3H H3C10
## 17: HIST1H4C H4C3
## 18: HIST2H2BF H2BC18
## 19: KIAA0391 PRORP
## 20: QARS EPRS1
## 21: SEPT6 SEPTIN6
## 22: ARNTL BMAL1
## 23: C12orf65 MTRFR
## 24: C16orf72 HAPSTR1
## 25: CCDC84 CENATAC
## 26: DOPEY2 DOP1B
## 27: FAM126B HYCC2
## 28: FAM160B1 FHIP2A
## 29: H1FX H1-10
## 30: H2AFJ H2AJ
## 31: HEXDC HEXD
## 32: HIST1H1C H1-2
## 33: HIST1H1D H1-3
## 34: HIST1H1E H1-4
## 35: KIAA1109 BLTP1
## 36: KIAA1551 RESF1
## 37: MKL1 MRTFA
## 38: NARFL CIAO3
## 39: SEPT2 SEPTIN6
## 40: TARSL2 TARS3
## 41: TMEM8A PGAP6
## 42: WDR60 DYNC2I1
## sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma), gene_symbol := sym_limma]
dim(gene_info)## [1] 1649 3
## sym_in_data sym_limma gene_symbol
## 1: ABLIM1 ABLIM1 ABLIM1
## 2: AC004687.1 <NA> AC004687.1
## 3: AC004854.2 <NA> AC004854.2
## 4: AC007384.1 <NA> AC007384.1
## 5: AC007952.4 <NA> AC007952.4
## t1
## 1 2
## 1647 1
## sym_in_data sym_limma gene_symbol
## 1: SEPT6 SEPTIN6 SEPTIN6
## 2: SEPT2 SEPTIN6 SEPTIN6
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
gmtfile[["immune"]] = "../Annotation/c7.all.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp" "immune"
## reactome go_bp immune
## 1692 7647 5219
Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
##
## $immune
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5 162 193 197 199 199 200 200 200 200 1992
## [1] 1649 3
max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol")
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.1)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=81)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "CD83" "RHOC" "RPL41" "TLE4" "ASCL2" "CD226" "GNLY" "MKLN1"
## [9] "PLAC8" "PRR5L" "PTPN4" "SPN" "THADA" "TMSB10" "TMSB4X" "UVRAG"
## [17] "VPS18" "VPS39" "XPO6" "YPEL5" "ZZEF1"
## [1] 2
## [1] "DTHD1" "GSTM1" "NT5DC1" "SLC27A5" "SLC4A4" "TRAV8-4" "ZNF862"
## [8] "ADCY7" "ARAP2" "BICRAL" "DIAPH2" "DMTF1" "GPR141" "MCTP2"
## [15] "MIAT" "MTERF2" "MYBL1" "NFATC3" "NLRC3" "TUT7" "UNC13D"
## [22] "XIST" "ZNF83"
## [1] 3
## [1] "APMAP" "CD84" "CMC1" "FAM118A" "FCER1G" "ICAM3"
## [7] "KLRF1" "KLRG1" "LEPROTL1" "LETMD1" "LRRC23" "NCR1"
## [13] "RTN3" "SH2D1A" "THAP9-AS1" "TMEM107" "TMEM42" "MCOLN2"
## [19] "PATL2" "PCSK7" "RASA3" "SLFN5"
## [1] 4
## [1] "ARHGAP9" "CYB5D2" "HLA-DMB" "INTS8" "KLRB1" "MZT2A"
## [7] "PDE3B" "RCSD1" "ABCC1" "AHCTF1" "DOPEY2" "ENTPD4"
## [13] "HLA-DQA1" "KLRD1" "LPCAT1" "PNPLA6" "PTPN7" "SLC38A10"
## [19] "ST6GAL1" "TAP2" "UGGT1"
## [1] 5
## [1] "ACTR1B" "ATP5MG" "COQ7" "CPNE1" "FAM102A" "GLRX5"
## [7] "MARCKSL1" "MPST" "NMT2" "RACK1" "UIMC1" "WDR86"
## [13] "DNAJB14" "GDPD5" "HERC3" "HERC6" "KIAA0232" "NUP210"
## [19] "R3HCC1L" "ZNF335" "ZNF800"
## [1] 6
## [1] "AC245297.3" "AL139246.5" "BBS9" "CRTAM" "CXorf57"
## [6] "EOMES" "HIST1H3H" "MFNG" "NUAK2" "PITPNC1"
## [11] "TRAV12-2" "TRAV38-2DV8" "TRBV3-1" "TRBV6-2" "TRBV6-5"
## [16] "CYTOR" "FAM126B" "GK5" "GPR174" "NRDC"
## [21] "OGA" "PARP15" "PIK3R5"
## [1] 7
## [1] "NUCB2" "PAIP2" "PDLIM1" "PTGER4" "RPL22L1" "STMN3"
## [7] "CWC25" "DENND4C" "GIGYF1" "GPANK1" "HELZ" "KIF13B"
## [13] "L3HYPDH" "MAN2C1" "RNMT" "SCAF8" "SECISBP2" "TIMP1"
## [19] "ZCCHC2"
## [1] 8
## [1] "C10orf91" "ANKRD36B" "ANKRD36C" "C16orf72" "CD46" "CHD9"
## [7] "CROCC" "DGKD" "EML4" "MIGA1" "RNF19A" "RPS6KA5"
## [13] "RSAD2" "RUBCN" "STAT4" "STK10" "SYNE1" "UBE2H"
## [19] "UBR2" "VPS13C" "ZNF493" "ZNF708"
## [1] 9
## [1] "ALOX5AP" "HDHD3" "KLRK1" "MATK" "TMEM134" "ANKRD12" "BTBD9"
## [8] "CST7" "GZMA" "GZMB" "IRF9" "KLF3" "LILRB1" "MYO1F"
## [15] "NKG7" "RNF125" "SPON2" "SRGN" "TMEM181" "UCP2" "ZFAND3"
## [1] 10
## [1] "AC008555.5" "AC044849.1" "AC083798.2" "AL135791.1" "COQ8A"
## [6] "FAM213B" "HIKESHI" "MTRNR2L8" "NBPF14" "PCMTD2"
## [11] "PRAG1" "RGL4" "TOX" "TRAV13-1" "TRAV14DV4"
## [16] "TRAV5" "TRBV7-2" "TRBV7-9" "TRGV5" "TRGV7"
## [21] "WARS2" "ZNF749"
## [1] 12
## [1] "BTG1" "HIST1H4C" "ID2" "JADE1" "LDLRAP1" "MSC"
## [7] "PNRC1" "WDR54" "ZNF575" "ARRDC3" "BRPF1" "COX19"
## [13] "GCN1" "GON4L" "KAT6B" "MAPK8IP3" "PHF14" "PKD1"
## [19] "RORA" "USP16" "ZNF292"
## [1] 13
## [1] "AC004687.1" "AC004854.2" "AC015982.1" "AC020911.2" "AC083880.1"
## [6] "AC091271.1" "AC103591.3" "AF213884.3" "AL357060.1" "AL451085.1"
## [11] "AL627171.1" "ARF4-AS1" "ATP2B1-AS1" "C6orf99" "HELQ"
## [16] "HIPK1-AS1" "KCNQ1OT1" "LINC01465" "MZF1-AS1" "OSER1-DT"
## [21] "PGGHG" "NEK9"
## [1] 14
## [1] "AOAH" "CCL4L2" "TRAV3" "TRG-AS1" "TRGV8" "TRGV9"
## [7] "CARD11" "CARD16" "EPSTI1" "FCRL6" "FGL2" "ITM2A"
## [13] "LINC02384" "NECAP1" "PTPRJ" "TRAV9-2" "TRDC" "TRDV1"
## [19] "TRGC2" "TRGV4" "TTC38" "XCL2"
## [1] 15
## [1] "ASAH1" "COMMD6" "COTL1" "ITGB1BP1" "LAPTM5" "NSUN6"
## [7] "PTPRCAP" "TPGS2" "CCNH" "CD2" "CD52" "CD8A"
## [13] "CD8B" "ITK" "LY6E" "PRSS23" "RHOH" "SBK1"
## [19] "SLC35F5" "TRAC" "TRBC2" "ZDHHC20"
## [1] 16
## [1] "TPRKB" "BDP1" "CHD1" "DHX29" "HELZ2" "HEXDC" "IFI44"
## [8] "IFIT2" "IFIT3" "KLHDC4" "MSI2" "MX1" "NEMF" "OAS3"
## [15] "PHACTR4" "PLA2G6" "REXO1" "RNF157" "RNPC3" "SPOCK2" "VAV3"
## [22] "ZC3H7B"
## [1] 17
## [1] "IL6R" "SERINC5" "TRBV6-1" "ABCA5" "ABR"
## [6] "AC020659.1" "CCDC84" "CPPED1" "DDX3Y" "EIF1AY"
## [11] "ENOSF1" "IL6ST" "KDM5D" "MICAL2" "OSM"
## [16] "RPS4Y1" "SBNO2" "SIDT1" "TRBV4-2" "ZMIZ2"
## [21] "ZNF236" "ZNF652"
## [1] 18
## [1] "ARHGAP45" "CEMIP2" "CRYBG1" "FAM133B" "MX2"
## [6] "OAS2" "PIK3CD" "PPP4R3B" "PREX1" "PUM3"
## [11] "RIPOR2" "S100A12" "SAMD9L" "TENT5C" "THUMPD3-AS1"
## [16] "TMEM131L" "TRANK1" "TRAV19" "TRAV27" "TRBV11-2"
## [21] "TRBV2" "TUT4"
## [1] 19
## [1] "AMD1" "CD27" "CREBL2" "CYB561A3" "EI24" "GIMAP1"
## [7] "GLTP" "IER3" "IFRD1" "KIR3DL2" "LIME1" "MZF1"
## [13] "NELL2" "PDE7A" "PPP1R15B" "SLC38A1" "TMEM204" "TSPYL4"
## [19] "LTBP4" "TRIM38" "VPS13A" "ZBTB40"
## [1] 20
## [1] "RGCC" "ACOX1" "BTN3A1" "CAST" "CCDC88C" "CELF2"
## [7] "DDHD1" "KDM5A" "MTMR6" "NCKAP1L" "NLRC5" "PCYT1A"
## [13] "PRKCH" "RAP1GAP2" "RASGRP1" "SPG11" "SYNRG" "TAOK1"
## [19] "TAOK3" "TIPARP" "ZEB2"
## [1] 21
## [1] "ID1" "RGS1" "AC092683.1" "AP005482.1" "ATAD2B"
## [6] "BMT2" "DOCK10" "ETFDH" "FAM78A" "GABPB2"
## [11] "GRK2" "HRH2" "IGKV3-15" "LINC02256" "MARF1"
## [16] "MINDY2" "NBEAL2" "POLR2J3-1" "SEC14L1" "THAP5"
## [21] "Z93930.2" "ZNF808"
## [1] 22
## [1] "ARL4A" "ABCA7" "CAPNS1" "ELMO1" "ERICH1" "FAM53B"
## [7] "FNBP1" "HSH2D" "IFI44L" "IL2RG" "IRAK4" "KCNAB2"
## [13] "KIAA1551" "KIAA2026" "KLF6" "PNPLA8" "PRDM2" "SENP7"
## [19] "TTC14" "WASL" "XAF1"
## [1] 23
## [1] "AC012645.3" "AC027644.3" "AC087623.3" "AK5" "AL118516.1"
## [6] "BX284668.6" "CHRM3-AS2" "FXYD7" "IGLV1-44" "INTS6L"
## [11] "KMT2E-AS1" "LINC00402" "LINC00649" "LST1" "MAP3K2"
## [16] "MATR3-1" "PDCD4-AS1" "RETREG1" "SNHG15" "TRAV21"
## [21] "TRAV8-2" "TRAV8-3"
## [1] 24
## [1] "C12orf45" "CAMK4" "CRLF3" "GCH1" "PLK2" "ZNF10"
## [7] "ANKRD44" "EHMT1" "FRYL" "MBD5" "PIGF" "POLH"
## [13] "PPP6R2" "PRR14L" "RLF" "SETD2" "SETX" "SP3"
## [19] "USP34" "WDR7" "ZNF407"
## [1] 25
## [1] "AL136454.1" "ATP5F1A" "CCNI" "COA1" "EFCAB2"
## [6] "FAM173A" "FCMR" "FCRL3" "GCSAM" "GTF3A"
## [11] "ITGAE" "RTRAF" "TRBC1" "ADGRE5" "ARHGAP30"
## [16] "CD38" "CTSW" "IFITM2" "MT2A" "MYO1G"
## [21] "SLA2" "ZNF683"
## [1] 26
## [1] "AIF1" "CD28" "YPEL3" "ANKRD49" "CASP10" "CFLAR"
## [7] "ETNK1" "FNDC3B" "GCA" "GPATCH2L" "H6PD" "IGHA1"
## [13] "LSS" "NCOA7" "PHF11" "PRKX" "PTGDS" "SETD5"
## [19] "WDTC1"
## [1] 27
## [1] "GNAQ" "NXT2" "AC016831.7" "ADHFE1" "AKNA"
## [6] "APOL6" "ARL4C" "ELMOD3" "GBP1" "GBP5"
## [11] "GNPTAB" "GPR132" "IFI27" "INPP4A" "ISG20"
## [16] "PDZD4" "PPP1R16B" "RAB27B" "SLFN12L" "SYTL3"
## [21] "TTC16"
## [1] 28
## [1] "BTG2" "C12orf10" "C12orf57" "CCNL1" "GSTM4" "KCTD7"
## [7] "MAP3K8" "MAPRE2" "NELFCD" "NEU1" "PTRHD1" "RPS26"
## [13] "RSRP1" "SEPT6" "SMDT1" "TGIF1" "ZFP36L1" "ACAP3"
## [19] "PARP4" "TEP1"
## [1] 29
## [1] "AC016405.3" "AC087239.1" "AC245014.3" "ANXA2R" "CITED2"
## [6] "CSKMT" "CXorf40A" "IER5" "IGKV3-20" "ILF3-DT"
## [11] "NOCT" "PIK3IP1" "SDR42E2" "SLC2A3" "SLC38A2"
## [16] "STK17A" "TC2N" "TRBV28" "WSB1" "Z93241.1"
## [21] "ZFAS1" "MALAT1"
## [1] 30
## [1] "BACH2" "CSRNP1" "EGR1" "EPS8" "FOSB" "MYLIP" "NOSIP" "NR1D1"
## [9] "NR4A2" "NR4A3" "RCAN3" "SELL" "SNHG12" "TCF7" "TXK" "CYTH1"
## [17] "DUS1L" "JUND" "MIDN" "SCRN3" "VCAN"
## [1] 31
## [1] "ASL" "CLDND1" "CXXC5" "GATA3" "PAPSS1" "RAB33B" "SESN1"
## [8] "SESN2" "TBCCD1" "TIGIT" "CSNK1G2" "ERAP2" "GALNT3" "ITGAM"
## [15] "KIR2DL3" "PYROXD1" "RAPGEF1" "RUFY2" "SZT2" "TBX21" "VPS13B"
## [22] "YPEL1" "ZDHHC5"
## [1] 32
## [1] "NT5E" "TBC1D17" "AFF1" "AFF4" "ARHGAP4" "BAZ2A" "CEP164"
## [8] "CRNKL1" "LRRFIP1" "LUC7L3" "NKTR" "PNN" "PPIG" "PPIL2"
## [15] "SRSF10" "SRSF11" "WDR60" "YTHDC1"
## [1] 33
## [1] "ZC3H12A" "B4GALT1" "BCL9L" "C2CD3" "CAPN15" "EHBP1L1" "LONP2"
## [8] "LPIN1" "NAA25" "NFKBIZ" "PDE4B" "PDE4D" "PIM1" "RALGAPB"
## [15] "RIC3" "STK17B" "TBC1D2B" "TOB1" "UTY" "ZBTB20"
## [1] 34
## [1] "GALNT11" "ADGRG1" "ARHGAP10" "CCL4" "CES1" "CX3CR1"
## [7] "ERBIN" "FGFBP2" "GALNT10" "GALNT2" "ITGAL" "LAG3"
## [13] "MPPE1" "MYO9B" "PEX1" "PEX26" "PLEK" "SEMA4D"
## [19] "ST8SIA4" "SUSD1" "TMEM8A"
## [1] 35
## [1] "HMBOX1" "KIF9" "ANKRD36" "AP3B1" "AP3M2" "ARAP1" "ARID5B"
## [8] "ATG2A" "ATG2B" "CLEC16A" "CREBZF" "FAM13B" "GPRIN3" "HECTD4"
## [15] "INO80" "INO80D" "INPP5D" "KLF2" "MKL1" "NARFL" "NFE2L1"
## [22] "PIP4K2B" "ZNF557"
## [1] 36
## [1] "AC025164.1" "AL121944.1" "AL138963.3" "ARMH1" "C6orf48"
## [6] "CCR7" "INPP4B" "JAML" "LINC02273" "LRRN3"
## [11] "LTB" "NPIPB4" "NUP58" "TCEA3" "TMIGD2"
## [16] "TNFRSF25" "TRABD2A" "TRAV1-2" "TRBV9" "OXNAD1"
## [21] "PARP11" "PCED1B"
## [1] 37
## [1] "AC007952.4" "AC119396.1" "ALKBH7" "BNIP3L" "CD40LG"
## [6] "CMTM7" "DYRK4" "EPB41L4A-AS1" "EPHX2" "GADD45B"
## [11] "GZMK" "HIBADH" "MCUB" "NOP53" "RGS10"
## [16] "SNHG8" "TCP11L2" "TESPA1" "TRBV20-1" "ZFAND1"
## [21] "ITPR2" "LINC02446"
## [1] 38
## [1] "CST3" "MAN2B1" "SAE1" "TRAT1" "ATP2B4" "CCDC112"
## [7] "CMKLR1" "CTSC" "DOCK11" "FAM169A" "LNPEP" "LRRC8A"
## [13] "PARP14" "RAB3GAP2" "SLC4A7" "SLK" "TMEM127" "TTC17"
## [19] "VPS13D" "ZNF276"
## [1] 39
## [1] "ABCC10" "ARHGEF3" "COL6A2" "COL6A3" "DDX60L"
## [6] "DENND4B" "EIF4E3" "HECA" "HPS4" "LAIR2"
## [11] "N4BP1" "NUTM2B-AS1" "ODF3B" "SUSD6" "TRAV12-3"
## [16] "TRAV17" "TRAV4" "TRBV7-6" "TRGV10" "TSPAN32"
## [21] "TTTY15" "XCL1" "ZBP1"
## [1] 40
## [1] "AC007384.1" "AC025171.3" "ARRDC2" "NT5C3B" "PRR7"
## [6] "SNHG9" "AC116407.2" "ARHGEF9" "BROX" "CHD6"
## [11] "DDIT4" "GPHN" "HIPK1" "IQCG" "KIAA1109"
## [16] "PCNX1" "PSMA3-AS1" "SLC16A1-AS1" "SLCO3A1" "SLF2"
## [21] "SPATA13" "TARSL2" "VTI1A"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_1"
## [1] "CD83" "RHOC" "RPL41" "TLE4" "ASCL2" "CD226" "GNLY" "MKLN1"
## [9] "PLAC8" "PRR5L" "PTPN4" "SPN" "THADA" "TMSB10" "TMSB4X" "UVRAG"
## [17] "VPS18" "VPS39" "XPO6" "YPEL5" "ZZEF1"
## $reactome
## category over_represented_pvalue
## 895 sars cov 2 modulates autophagy 2.230272e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 895 1 3 3 0.002593807
##
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 4354 snare complex assembly 2.79997e-06 1
## numDEInCat numInCat FDR
## 4354 3 3 0.01313466
##
## [1] "set_3"
## [1] "APMAP" "CD84" "CMC1" "FAM118A" "FCER1G" "ICAM3"
## [7] "KLRF1" "KLRG1" "LEPROTL1" "LETMD1" "LRRC23" "NCR1"
## [13] "RTN3" "SH2D1A" "THAP9-AS1" "TMEM107" "TMEM42" "MCOLN2"
## [19] "PATL2" "PCSK7" "RASA3" "SLFN5"
## $reactome
## category
## 435 immunoregulatory interactions between a lymphoid and a non lymphoid cell
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 435 8.235374e-06 0.9999998 5 34
## FDR
## 435 0.00957774
##
## [1] "set_9"
## [1] "ALOX5AP" "HDHD3" "KLRK1" "MATK" "TMEM134" "ANKRD12" "BTBD9"
## [8] "CST7" "GZMA" "GZMB" "IRF9" "KLF3" "LILRB1" "MYO1F"
## [15] "NKG7" "RNF125" "SPON2" "SRGN" "TMEM181" "UCP2" "ZFAND3"
## $immune
## category
## 4250 gse45739 unstim vs acd3 acd28 stim nras ko cd4 tcell dn
## 4981 kazmin pbmc p falciparum rtss as01 age unknown correlated with protection 56dy ne
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4250 3.623625e-06 0.9999998 7 54
## 4981 6.626185e-06 0.9999998 5 22
## FDR
## 4250 0.01689015
## 4981 0.01689015
##
## [1] "set_15"
## [1] "ASAH1" "COMMD6" "COTL1" "ITGB1BP1" "LAPTM5" "NSUN6"
## [7] "PTPRCAP" "TPGS2" "CCNH" "CD2" "CD52" "CD8A"
## [13] "CD8B" "ITK" "LY6E" "PRSS23" "RHOH" "SBK1"
## [19] "SLC35F5" "TRAC" "TRBC2" "ZDHHC20"
## $go_bp
## category over_represented_pvalue
## 4477 t cell receptor signaling pathway 1.445094e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 4477 0.9999993 6 43 0.06778935
##
## [1] "set_16"
## [1] "TPRKB" "BDP1" "CHD1" "DHX29" "HELZ2" "HEXDC" "IFI44"
## [8] "IFIT2" "IFIT3" "KLHDC4" "MSI2" "MX1" "NEMF" "OAS3"
## [15] "PHACTR4" "PLA2G6" "REXO1" "RNF157" "RNPC3" "SPOCK2" "VAV3"
## [22] "ZC3H7B"
## $immune
## category
## 1342 gse18791 unstim vs newcatsle virus dc 10h dn
## 5074 sobolev pbmc pandemrix age 18 64yo 7dy dn
## 1368 gse18893 tconv vs treg 24h culture dn
## 4081 gse42724 naive bcell vs plasmablast up
## 1338 gse18791 ctrl vs newcastle virus dc 6h dn
## 5055 querec pbmc yf 17d vaccine age 18 45yo 3dy up
## 5056 querec pbmc yf 17d vaccine age 18 45yo 7dy up
## 1453 gse19888 adenosine a3r inh vs act with inhibitor pretreatment in mast cell up
## 10 erwin cohen blood tc 83 age 23 48yo vaccinated vs control 2dy up
## 4874 gse9960 gram neg vs gram neg and pos sepsis pbmc up
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1342 3.851459e-07 1.0000000 8 55
## 5074 7.535735e-07 1.0000000 5 14
## 1368 3.311437e-06 0.9999999 6 34
## 4081 6.338755e-06 0.9999996 7 55
## 1338 1.595504e-05 0.9999989 7 63
## 5055 1.606477e-05 0.9999994 5 24
## 5056 1.606477e-05 0.9999994 5 24
## 1453 2.393285e-05 0.9999986 6 44
## 10 2.771849e-05 0.9999983 6 45
## 4874 3.128033e-05 0.9999986 5 28
## FDR
## 1342 0.001920859
## 5074 0.001920859
## 1368 0.005627235
## 4081 0.008078743
## 1338 0.011699744
## 5055 0.011699744
## 5056 0.011699744
## 1453 0.015251207
## 10 0.015700984
## 4874 0.015946710
##
## [1] "set_17"
## [1] "IL6R" "SERINC5" "TRBV6-1" "ABCA5" "ABR"
## [6] "AC020659.1" "CCDC84" "CPPED1" "DDX3Y" "EIF1AY"
## [11] "ENOSF1" "IL6ST" "KDM5D" "MICAL2" "OSM"
## [16] "RPS4Y1" "SBNO2" "SIDT1" "TRBV4-2" "ZMIZ2"
## [21] "ZNF236" "ZNF652"
## $reactome
## category over_represented_pvalue
## 478 interleukin 6 family signaling 2.671849e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 478 0.9999998 3 8 0.03107361
##
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 4122 response to interleukin 6 1.242271e-05 0.9999999
## numDEInCat numInCat FDR
## 4122 3 5 0.05827493
##
## [1] "set_18"
## [1] "ARHGAP45" "CEMIP2" "CRYBG1" "FAM133B" "MX2"
## [6] "OAS2" "PIK3CD" "PPP4R3B" "PREX1" "PUM3"
## [11] "RIPOR2" "S100A12" "SAMD9L" "TENT5C" "THUMPD3-AS1"
## [16] "TMEM131L" "TRANK1" "TRAV19" "TRAV27" "TRBV11-2"
## [21] "TRBV2" "TUT4"
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 2154 neutrophil chemotaxis 1.564504e-05 0.9999997
## 2160 neutrophil migration 2.912363e-05 0.9999993
## 1047 granulocyte chemotaxis 3.103883e-05 0.9999992
## 1050 granulocyte migration 5.931136e-05 0.9999983
## numDEInCat numInCat FDR
## 2154 4 19 0.04853439
## 2160 4 22 0.04853439
## 1047 4 22 0.04853439
## 1050 4 26 0.06955740
##
## [1] "set_19"
## [1] "AMD1" "CD27" "CREBL2" "CYB561A3" "EI24" "GIMAP1"
## [7] "GLTP" "IER3" "IFRD1" "KIR3DL2" "LIME1" "MZF1"
## [13] "NELL2" "PDE7A" "PPP1R15B" "SLC38A1" "TMEM204" "TSPYL4"
## [19] "LTBP4" "TRIM38" "VPS13A" "ZBTB40"
## $immune
## category over_represented_pvalue
## 1977 gse22886 naive tcell vs monocyte up 1.476627e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 1977 0.9999989 7 64 0.07527844
##
## [1] "set_30"
## [1] "BACH2" "CSRNP1" "EGR1" "EPS8" "FOSB" "MYLIP" "NOSIP" "NR1D1"
## [9] "NR4A2" "NR4A3" "RCAN3" "SELL" "SNHG12" "TCF7" "TXK" "CYTH1"
## [17] "DUS1L" "JUND" "MIDN" "SCRN3" "VCAN"
## $reactome
## category over_represented_pvalue
## 645 nuclear receptor transcription pathway 5.987482e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 645 0.9999994 3 6 0.06963441
##
## $immune
## category
## 4345 gse4984 lps vs vehicle ctrl treated dc up
## 3878 gse40666 stat1 ko vs stat4 ko cd8 tcell with ifna stim 90min dn
## 708 gse15733 bm vs spleen memory cd4 tcell dn
## 3537 gse37605 foxp3 fusion gfp vs ires gfp treg c57bl6 up
## 5021 nakaya pbmc fluarix fluvirin age 18 50yo 7dy dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4345 8.073533e-06 0.9999997 5 26
## 3878 3.607021e-05 0.9999984 5 26
## 708 5.836425e-05 0.9999970 5 33
## 3537 5.870079e-05 0.9999971 5 28
## 5021 8.787659e-05 0.9999917 7 76
## FDR
## 4345 0.04115887
## 3878 0.07481416
## 708 0.07481416
## 3537 0.07481416
## 5021 0.08959897
##
## [1] "set_31"
## [1] "ASL" "CLDND1" "CXXC5" "GATA3" "PAPSS1" "RAB33B" "SESN1"
## [8] "SESN2" "TBCCD1" "TIGIT" "CSNK1G2" "ERAP2" "GALNT3" "ITGAM"
## [15] "KIR2DL3" "PYROXD1" "RAPGEF1" "RUFY2" "SZT2" "TBX21" "VPS13B"
## [22] "YPEL1" "ZDHHC5"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 47 amino acids regulate mtorc1 4.312411e-05 0.9999996
## numDEInCat numInCat FDR
## 47 3 6 0.05015334
##
## [1] "set_32"
## [1] "NT5E" "TBC1D17" "AFF1" "AFF4" "ARHGAP4" "BAZ2A" "CEP164"
## [8] "CRNKL1" "LRRFIP1" "LUC7L3" "NKTR" "PNN" "PPIG" "PPIL2"
## [15] "SRSF10" "SRSF11" "WDR60" "YTHDC1"
## $reactome
## category over_represented_pvalue
## 579 mrna splicing 2.449222e-07
## 721 processing of capped intron containing pre mrna 8.173826e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 579 1 7 38 0.0002848445
## 721 1 7 45 0.0004753080
##
## $go_bp
## category over_represented_pvalue
## 4255 rna splicing 3.815935e-07
## 4395 spliceosomal complex assembly 1.192757e-05
## 1584 mrna splice site recognition 7.284369e-05
## 4257 rna splicing via transesterification reactions 8.480068e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 4255 1.0000000 8 72 0.001790055
## 4395 0.9999998 4 14 0.027976117
## 1584 0.9999991 3 8 0.099449994
## 4257 0.9999955 5 43 0.099449994
##
## [1] "set_34"
## [1] "GALNT11" "ADGRG1" "ARHGAP10" "CCL4" "CES1" "CX3CR1"
## [7] "ERBIN" "FGFBP2" "GALNT10" "GALNT2" "ITGAL" "LAG3"
## [13] "MPPE1" "MYO9B" "PEX1" "PEX26" "PLEK" "SEMA4D"
## [19] "ST8SIA4" "SUSD1" "TMEM8A"
## $reactome
## category over_represented_pvalue
## 654 o linked glycosylation of mucins 3.406216e-05
## 653 o linked glycosylation 6.745152e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 654 0.9999998 3 5 0.03922306
## 653 0.9999993 3 6 0.03922306
##
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 2230 o glycan processing 1.881402e-05 0.9999999
## 1031 glycosylation 1.935866e-05 0.9999996
## numDEInCat numInCat FDR
## 2230 3 5 0.04540574
## 1031 4 14 0.04540574
##
## $immune
## category over_represented_pvalue
## 4252 gse45739 unstim vs acd3 acd28 stim wt cd4 tcell dn 1.901911e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 4252 0.9999986 7 70 0.09695942
##
## [1] "set_36"
## [1] "AC025164.1" "AL121944.1" "AL138963.3" "ARMH1" "C6orf48"
## [6] "CCR7" "INPP4B" "JAML" "LINC02273" "LRRN3"
## [11] "LTB" "NPIPB4" "NUP58" "TCEA3" "TMIGD2"
## [16] "TNFRSF25" "TRABD2A" "TRAV1-2" "TRBV9" "OXNAD1"
## [21] "PARP11" "PCED1B"
## $immune
## category over_represented_pvalue
## 2391 gse26495 naive vs pd1high cd8 tcell up 4.581605e-06
## 2393 gse26495 naive vs pd1low cd8 tcell up 8.116493e-06
## 142 gse11057 naive vs cent memory cd4 tcell up 5.570191e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 2391 0.9999999 5 30 0.02068894
## 2393 0.9999998 5 33 0.02068894
## 142 0.9999984 4 25 0.09465612
##
## [1] "set_39"
## [1] "ABCC10" "ARHGEF3" "COL6A2" "COL6A3" "DDX60L"
## [6] "DENND4B" "EIF4E3" "HECA" "HPS4" "LAIR2"
## [11] "N4BP1" "NUTM2B-AS1" "ODF3B" "SUSD6" "TRAV12-3"
## [16] "TRAV17" "TRAV4" "TRBV7-6" "TRGV10" "TSPAN32"
## [21] "TTTY15" "XCL1" "ZBP1"
## $reactome
## category
## 159 collagen biosynthesis and modifying enzymes
## 160 collagen chain trimerization
## 72 assembly of collagen fibrils and other multimeric structures
## 162 collagen formation
## 590 ncam1 interactions
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 159 9.184822e-05 1.0000000 2 2
## 160 9.184822e-05 1.0000000 2 2
## 72 2.146121e-04 0.9999995 2 3
## 162 2.146121e-04 0.9999995 2 3
## 590 2.835424e-04 0.9999992 2 3
## FDR
## 159 0.05340974
## 160 0.05340974
## 72 0.06239846
## 162 0.06239846
## 590 0.06595195
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8958444 478.5 16391124 875.4 NA 16391124 875.4
## Vcells 19169726 146.3 73326430 559.5 65536 91658037 699.3
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0
## [2] GenomicFeatures_1.50.4
## [3] GenomicRanges_1.50.2
## [4] GenomeInfoDb_1.34.9
## [5] org.Hs.eg.db_3.16.0
## [6] AnnotationDbi_1.60.2
## [7] IRanges_2.32.0
## [8] S4Vectors_0.36.2
## [9] Biobase_2.58.0
## [10] BiocGenerics_0.44.0
## [11] goseq_1.50.0
## [12] geneLenDataBase_1.34.0
## [13] BiasedUrn_2.0.10
## [14] fgsea_1.24.0
## [15] biomaRt_2.54.1
## [16] limma_3.54.2
## [17] tidyr_1.3.0
## [18] ggpubr_0.6.0
## [19] ggplot2_3.4.2
## [20] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 tools_4.2.3
## [9] backports_1.4.1 bslib_0.4.2
## [11] utf8_1.2.3 R6_2.5.1
## [13] mgcv_1.8-42 DBI_1.1.3
## [15] colorspace_2.1-0 withr_2.5.0
## [17] tidyselect_1.2.0 prettyunits_1.1.1
## [19] bit_4.0.5 curl_5.0.1
## [21] compiler_4.2.3 cli_3.6.1
## [23] xml2_1.3.4 DelayedArray_0.24.0
## [25] rtracklayer_1.58.0 sass_0.4.5
## [27] scales_1.2.1 rappdirs_0.3.3
## [29] Rsamtools_2.14.0 stringr_1.5.0
## [31] digest_0.6.31 rmarkdown_2.21
## [33] XVector_0.38.0 pkgconfig_2.0.3
## [35] htmltools_0.5.5 MatrixGenerics_1.10.0
## [37] dbplyr_2.3.2 fastmap_1.1.1
## [39] rlang_1.1.0 rstudioapi_0.14
## [41] RSQLite_2.3.1 BiocIO_1.8.0
## [43] jquerylib_0.1.4 generics_0.1.3
## [45] jsonlite_1.8.4 BiocParallel_1.32.6
## [47] dplyr_1.1.2 car_3.1-2
## [49] RCurl_1.98-1.12 magrittr_2.0.3
## [51] GO.db_3.16.0 GenomeInfoDbData_1.2.9
## [53] Matrix_1.6-4 Rcpp_1.0.10
## [55] munsell_0.5.0 fansi_1.0.4
## [57] abind_1.4-5 lifecycle_1.0.3
## [59] stringi_1.7.12 yaml_2.3.7
## [61] carData_3.0-5 SummarizedExperiment_1.28.0
## [63] zlibbioc_1.44.0 BiocFileCache_2.6.1
## [65] grid_4.2.3 blob_1.2.4
## [67] parallel_4.2.3 crayon_1.5.2
## [69] lattice_0.20-45 splines_4.2.3
## [71] Biostrings_2.66.0 cowplot_1.1.1
## [73] hms_1.1.3 KEGGREST_1.38.0
## [75] knitr_1.44 pillar_1.9.0
## [77] rjson_0.2.21 ggsignif_0.6.4
## [79] codetools_0.2-19 fastmatch_1.1-3
## [81] XML_3.99-0.14 glue_1.6.2
## [83] evaluate_0.20 png_0.1-8
## [85] vctrs_0.6.2 gtable_0.3.3
## [87] purrr_1.0.1 cachem_1.0.7
## [89] xfun_0.39 broom_1.0.4
## [91] restfulr_0.0.15 rstatix_0.7.2
## [93] tibble_3.2.1 GenomicAlignments_1.34.1
## [95] memoise_2.0.1